<PAGE>

                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                  ------------

                                   FORM 10-Q/A
                                 AMENDMENT NO. 2

  [ X ]         QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934

                FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2000

                                       OR

   [ ]          TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934

                    FOR THE TRANSITION PERIOD FROM ___ TO ___

                        COMMISSION FILE NUMBER 000-23541


                                  NANOGEN, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)


                DELAWARE                                     33-0489621
     (State or other jurisdiction of                      (I.R.S. Employer
      incorporation or organization)                     Identification No.)


       10398 PACIFIC CENTER COURT, SAN DIEGO, CA              92121
       (Address of principal executive offices)            (Zip code)


                                 (858) 410-4600
              (Registrant's telephone number, including area code)


  Indicate by check mark whether the registrant (1) has filed all reports
  required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
  1934 during the preceding 12 months (or for such shorter period that the
  registrant was required to file such reports), and (2) has been subject to
  such filing requirements for the past 90 days.

                       YES     X            NO
                             ------             ------


AS OF NOVEMBER 11, 2000, 20,931,962 SHARES OF THE REGISTRANT'S COMMON STOCK WERE
OUTSTANDING.

<PAGE>

                                EXPLANATORY NOTE

         This Form 10-Q/A Quarterly Report for the period ending September 30,
2000 is being filed to amend the original From 10-Q Quarterly Report filed
November 14, 2000 to reflect the resolution of Confidential Treatment Requests
("CTRs") filed by Nanogen, Inc. with the Securities and Exchange Commission
("SEC") on December 23, 1999. These CTRs were filed in accordance with SEC
rules, pursuant to which Nanogen, Inc. requested confidential, non-public
treatment for certain portions of agreements including the agreement attached
hereto as Exhibit 10.18. Apart from disclosing previously redacted terms of this
agreement, there are no other substantive changes to the Form 10-Q Quarterly
Report as originally filed.

                           PART II - OTHER INFORMATION


ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K

      (a)  Exhibits

<TABLE>
<S>                 <C>
          10.1      First Amendment of Master Agreement between Registrant and BD, dated as of September 25, 2000*
          10.2      First Amendment of Collaborative  Research and Development and License Agreement  between  Registrant and BD,
                    dated as of September 25, 2000+*
          10.3      First Amendment of General Partnership Agreement between Registrant and BD, dated as of September 25, 2000+*
          10.4      First Amendment of License Agreement between Registrant and BD, dated as of September 25, 2000+*
          10.5      Partnership Product Commercialization License Agreement, dated as of September 25, 2000+*
          10.6      Collaboration  Agreement  between  Registrant  and Hitachi  Ltd.,  Nissei  Sangyo Co. Ltd. and Hitachi
                    Instruments Service Co. Ltd., (collectively the "Hitachi Parties"), dated July 26, 2000+*
          10.7      First Amendment to Reader, Loader and Cassette Low Cost Engineering and Manufacturing  Agreement between
                    Registrant and Hitachi, Ltd., dated July 26, 2000+*
          10.8      Common Stock Purchase Agreement between Registrant and the Hitachi Parties, dated July 26, 2000*
          10.9      Warrant to Purchase Common Stock between Registrant and Aventis Research and Technologies Verwaltungs,  GmbH,
                    dated September 22, 2000*
          10.10     First Amendment to Employment Agreement between Registrant and Howard C. Birndorf, dated as of July 28, 2000*
          10.11     First Amendment to Employment Agreement between Registrant and Kieran T. Gallahue, dated as of July 28, 2000*
          10.12     First Amendment to Employment Agreement between Registrant and Michael D. Moore, dated as of July 28, 2000*
          10.13     First Amendment to Employment Agreement between Registrant and James P. O'Connell, dated as of July 28, 2000*
          10.14     First Amendment to Employment Agreement between Registrant and George E. Bers, dated as of July 28, 2000*
          10.15     First Amendment to Employment Agreement between Registrant and Michael J. Heller, dated as of July 28, 2000*
          10.16     Letter Agreement between Registrant and Hoechst AG ("Hoechst"), dated December 4, 1997.+*
          10.17     Sponsored Research Agreement between Registrant and Prolinx, Inc., dated as of December 18, 1996+*
          10.18     Collaborative Research and Development Agreement between Registrant and Hoechst, dated December 3, 1998+
          27.1      Financial Data Schedule*
          ----------
</TABLE>

         + Confidential Treatment has been requested with respect to certain
           portions of this agreement.
         * Previously Filed.



      (b)  Reports on Form 8-K

           No Reports on Form 8-K were filed during the three months ended
September 30, 2000.


<PAGE>


                                  NANOGEN, INC.

                                   SIGNATURES


PURSUANT TO THE REQUIREMENTS OF THE SECURITIES EXCHANGE ACT OF 1934, THE
REGISTRANT HAS DULY CAUSED THIS REPORT TO BE SIGNED ON ITS BEHALF BY THE
UNDERSIGNED THEREUNTO DULY AUTHORIZED.


                                  NANOGEN, INC.



DATE                    MARCH 13, 2001          /S/ HOWARD C. BIRNDORF
                    ------------------------    --------------------------------
                                                HOWARD C. BIRNDORF
                                                CHAIRMAN OF THE BOARD AND CHIEF
                                                EXECUTIVE OFFICER
                                                (PRINCIPAL EXECUTIVE OFFICER)


DATE                    MARCH 13, 2001          /S/ KIERAN T. GALLAHUE
                    ------------------------    --------------------------------
                                                KIERAN T. GALLAHUE
                                                PRESIDENT, CHIEF FINANCIAL
                                                OFFICER AND TREASURER
                                                (PRINCIPAL FINANCIAL OFFICER)








<PAGE>



                                  NANOGEN, INC.
                                  EXHIBIT INDEX

<TABLE>
<CAPTION>

   EXHIBIT NO.                                             Description
<S>      <C>
10.1     First Amendment of Master Agreement between Registrant and BD, dated as of September 25,
         2000*
10.2     First Amendment of Collaborative Research and Development and License Agreement between
         Registrant and BD, dated as of September 25, 2000+*
10.3     First Amendment of General Partnership Agreement between Registrant and BD, dated as of
         September 25, 2000+*
10.4     First Amendment of License Agreement between Registrant and BD, dated as of September
         25, 2000+*
10.5     Partnership Product Commercialization License Agreement, dated as of September 25, 2000+*
10.6     Collaboration Agreement between Registrant and Hitachi, Ltd., Nissei Sangyo Co. Ltd. and
         Hitachi Instruments Service Co. Ltd., (collectively the "Hitachi Parties"), dated July
         26, 2000+*
10.7     First Amendment to Reader, Loader and Cassette Low Cost Engineering and Manufacturing
         Agreement between Registrant and Hitachi, Ltd., dated July 26, 2000+*
10.8     Common Stock Purchase Agreement between Registrant and the Hitachi Parties, dated July
         26, 2000*
10.9     Warrant to Purchase Common Stock between Registrant and Aventis Research and
         Technologies Verwaltungs, GmbH, dated September 22, 2000*
10.10    First Amendment to Employment Agreement between Registrant and Howard C. Birndorf, dated
         as of July 28, 2000*
10.11    First Amendment to Employment Agreement between Registrant and Kieran T. Gallahue, dated
         as of July 28, 2000*
10.12    First Amendment to Employment Agreement between Registrant and Michael D. Moore, dated
         as of July 28, 2000*
10.13    First Amendment to Employment Agreement between Registrant and James P. O'Connell, dated
         as of July 28, 2000*
10.14    First Amendment to Employment Agreement between Registrant and George E. Bers, dated as
         of July 28, 2000*
10.15    First Amendment to Employment Agreement between Registrant and Michael J. Heller, dated
         as of July 28, 2000*
10.16    Letter Agreement between Registrant and Hoechst AG ("Hoechst"), dated December 4, 1997+*
10.17    Sponsored Research Agreement between Registrant and Prolinx, Inc., dated as of December
         18, 1996+*
10.18    Collaborative Research and Development Agreement between Registrant and Hoechst, dated
         December 3, 1998+
27.1     Financial Data Schedule*
</TABLE>
----------------
         + Confidential Treatment has been requested with respect to
           certain portions of this agreement.
         * Previously Filed.